ArticleCell genomics2021
Molecular analysis of TCGA breast cancer histologic types.
Article in Cell genomics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 76 papers.
What it found
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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
76 citing papers in PubMed.
- A predictive endocrine resistance index accurately stratifies luminal breast cancer treatment responders and nonresponders.The Journal of clinical investigation · 2025Trial
- The spatially informed mFISHseq assay resolves biomarker discordance and predicts treatment response in breast cancer.Nature communications · 2025Trial
- FGFR1 Suppresses STING-Mediated Interferon Response in Endocrine Therapy-Resistant Breast Cancer.Cancer research communications · 2026Article
- ALPaCA: Adapting Llama for Pathology Context Analysis to enable slide-level question answering.Nature communications · 2026Article
- A β-Hydroxybutyrylation-FOXM1/CENPA Axis Links Ketone-Body Metabolism to Mitotic Transcription in Basal-like Breast Cancer.International journal of molecular sciences · 2026Article
- Using Deep Learning Models of Gene Regulation to Guide Drug Prioritization.Pharmaceuticals (Basel, Switzerland) · 2026Article
- Why biology must prioritize data reanalysis in the era of artificial intelligence.PLoS biology · 2026Article
- The clinical relevance of apocrine morphology in breast cancer depends on the estrogen receptor status.NPJ breast cancer · 2026Article
- Domain generalisation challenges in breast cancer molecular classification using foundation models: a cross-cohort exploratory study.Medical & biological engineering & computing · 2026Article
- Using Deep Learning Models of Gene Regulation to Guide Drug Prioritization.bioRxiv : the preprint server for biology · 2026Article
- Integrating breast tumour homologous recombination deficiency status to aid germline BRCA1 and BRCA2 variant classification.EBioMedicine · 2026Article
- Extending differential gene expression testing to handle genome aneuploidy in cancer.PLoS computational biology · 2026Article
- Single amino-acid differences define H2B variants and modify chromatin accessibility to induce EMT in breast cancer.Oncogene · 2026Article
- Genomic analysis of radiosensitivity in breast cancer : Identifying pathological determinants and assessing genomic-adjusted radiation dose (GARD) for personalized dose escalation.Strahlentherapie und Onkologie : Organ der Deutschen Rontgengesellschaft ... [et al] · 2026Article
- Sample size requirements for machine learning classification of binary outcomes in bulk RNA-Seq data.BMC bioinformatics · 2026Article
- Lactylation-mediated remodelling of the breast cancer microenvironment: single-cell multidimensional analysis and prognostic model construction.Frontiers in immunology · 2026Article
- DHL-11, a novel prieurianin-type limonoid isolated fromActa pharmaceutica Sinica. B · 2026Article
- Tumor necrosis associates with aggressive breast cancer features, increased hypoxia signaling and reduced patient survival.Scientific reports · 2025Article
- System analysis links SMARCD3 regulons to growth signaling and MEK inhibitor response in everolimus-resistant ER+ breast cancer cells.Cell reports. Medicine · 2025Article
- The tumor microenvironment of 14,837 breast cancers is associated with clinical outcome independently of genomic subtypes.Cell reports. Medicine · 2025Article
16 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
12 authors.
Funding
Abstract
Breast cancer is classified into multiple distinct histologic types, and many of the rarer types have limited characterization. Here, we extend The Cancer Genome Atlas Breast Cancer (TCGA-BRCA) dataset with additional histologic type annotations, in a total of 1063 breast cancers. We analyze this extended dataset to define transcriptomic and genomic profiles of six rare special histologic types: cribriform, micropapillary, mucinous, papillary, metaplastic, and invasive carcinoma with medullary pattern. We show the broader applicability of our constructed special histologic type gene signatures in the TCGA Pan-Cancer Atlas dataset with a predictive model that detects mucinous histologic type across cancers of other organ systems. Using a normal mammary cell differentiation score analysis, we order histologic types into a continuum from stem cell-like to luminal progenitor-like to mature luminal-like. Finally, we classify TCGA-BRCA into 12 consensus groups based on integrated genomic and histological features. We present a rich openly accessible resource of histologic and genomic characterization of TCGA-BRCA to enable studies of the range of breast cancers.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.